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Biomarker prediction analysis
Choose a precomputed gene knockout. For each biomarker metabolite we show the predicted maximal blood flux across a cohort of host-microbiome whole-body models in the healthy vs disease (knockout) state, tested for significance, separately for female and male.
Research & education only — these are model predictions across a sample cohort, not clinical or diagnostic results for any individual.
The idea. The germ-free whole-body models predict biomarkers from first principles — known human metabolism as encoded in the WBMs. But the gut microbiome within us contributes to host metabolism, so some of those first-principles biomarkers may no longer be robust once a microbiome is present. This page asks: which predicted biomarkers remain robust when the microbiome is considered, and how much do those robust predictions overlap with the clinically used biomarkers (IEMbase)?
box = median / IQR, whiskers = min–max, dots = models · stars = BH-FDR (*** q<.001, ** q<.01, * q<.05, ns) · ▲ higher / ▼ lower in knockout
Cohort descriptionwho is in the microbiome cohort
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Genome-scale reconstruction scopethe models the predictions were computed on
| Reconstruction | # reactions | # metabolites | # microbial species |
|---|
Microbiome-WBM counts reassembled from the database recipes (ADR-073); germ-free counts from the reference models. std = standard deviation.
Microbial composition & diversityacross the cohort's gut microbiome samples
Predicted biomarker fluxes: germ-free vs host-microbiome
Select a knockout.
Germ-free predictions (first principles)what known human metabolism alone predicts
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Outlier analysis
Select a knockout.
Outlier vs typical samples — microbiome metadata
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Biomarker distributions (healthy vs )
HM healthyHM knockout (host-microbiome cohort: box = median/IQR, whiskers = min–max, dots = models)· GF ref (germ-free, host-only) printed above each plot — often a different scale, shown for reference only⚠ microbial ≈N× GF= steep microbial contribution (HM ≥5× germ-free) — warrants mechanistic analysis